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README.md

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Config

This module contains python configuration files, which are imported by other modules within the repository

Protocol

Ad_config

Automate demultiplex configuration. Contains general settings, and the following classes collating the settings required per module:

  • AdEmailConfig
  • AdLoggerConfig
  • DemultiplexConfig
  • SWConfig
  • ToolboxConfig
  • URConfig

Log_msgs_config

Config file for logging module (imported by ad_logger module). Contains settings specific to logging. The LOG_MSGS dictionary contains both general messages which are used across multiple modules, and also logfile-specific messages:

  • Ad_email
  • Demultiplex
  • ss_validator
  • sw
  • backup

Panel_config

The panel config file contains the panel numbers and panel properties, which are used by the setoff_workflows script.

The PANEL_DICT is built up in stages using various other dictionaries to reduce repetition. The base dictionary is the DEFAULT_DICT, which is incorporated into the CAPTURE_PANEL_DICT, which are then imported into the PANEL_DICT. The dictionaries POLYEDGE_INPUTS and CONGENICA_CREDENTIALS are also imported into the PANEL_DICT.

Panel number lists are created from the PANEL_DICT, assimilating pan numbers from the PANEL_DICT which meet the required criteria to be included in that list.

  • SNP does not have R numbers (test_number) as it is an identity check for the GMS SMS
  • Panels for WES (analysed in Congenica) and TSO500 (analysed in QCII), and ArcherDX (analysed in Archer software), are applied at the point of analysis, so R and M numbers (test_number) for these are not listed below. These pan numbers do not necessarily refer to bed files but rather project configuration (e.g. DNAnexus instances, project layout etc.)
  • Development runs have two options for pan numbers, one for runs that require standard processing with bcl2fastq and one for runs that require manual processing as they have UMIs
Dictionary key Details
panel_name Name of capture panel
pipeline Name of pipeline
runtype Type of run
sample_prefix Expected string at front of sample name
capture_pan_num Pan number of capture panel bedfile (used for RPKM). False if RPKM not run
hsmetrics_bedfile bedfile filename, or False
sambamba_bedfile bedfile filename, or False. Coverage BED
variant_calling_bedfile bedfile filename, or False
FH True if requires PRS analysis, False if not
rpkm_bedfile bedfile filename, or False
capture_type Amplicon or Hybridisation
multiqc_coverage_level Value
clinical_coverage_depth Value, or False. Used as input for sambamba
coverage_min_basecall_qual Value or False. Sambamba minimum base quality
coverage_min_mapping_qual Value or False. Sambamba minimum mapping quality
masked_reference projectid:fileid, or False
test_number R or M number, or false if no specific number
congenica_project False = no upload. Number = normal. SFTP = sftp upload
congenica_credentials 'Viapath' or 'StG'. False = Congenica app not used
congenica_IR_template 'priority' or 'non-priority'. False = Congenica app not used
polyedge False if app not required, subdictionary containing app inputs if it is required
ed_readcount_bedfile False if app not required, panel bed file if required
ed_cnvcalling_bedfile None if app not required, R-number specific bedfile if required
dry_lab True if required to share with dry lab, None if not
dry_lab_only Used to determine whether to include the TSO pan number in the duty_csv pan number list
drylab_dnanexus_id False if not required to share with other users, user ID string if needs sharing
umis True if run has UMIs

Usage

This script is configured to be used as a module import as per the following examples:

from config import ad_config

Logging

No log is written to as this module contains only configuration files.

Testing

This module has no tests.